O.K. I tried a few things to connect Musescore to Pianoteq and could not make it work initially. I was able to make it work by turning off Portaudio. I am using KXStudio on Ubuntu 14.04, so it is simple for me to turn off Portaudio using a program called Cadence. If you don't have Cadence you could consider installing this program along with Catia and other tools by looking at KXStudio, though I do not know how this might or might affect your current setup. Alternatively, you might try uninstalling portaudio from your computer, if you don't need it or maybe disabling it by killing the process, though I don't know if that will create other trouble. From things I have read in the past, portaudio can be a problem in Linux audio.
All of that being said, there is another issue with Musescore where it does not play all of the notes through a midi connection, which happened to me when I got the midi connection working This issue is discussed here:
www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=15&ved=0CHkQFjAO&url=http%3A%2F%2Fmusescore.org%2Fnode%2F22814&ei=a8u9VP2zGfiPsQTw44FA&usg=AFQjCNEM5UluvopUaqSw3xvfKY5WrvAsuw
As others have suggested, you may not want to use Musescore. You could try Rosegarden if using musical notation is important to you as this program can work well with Pianoteq in my experience, though you might need the alsa midi bridge installed (a2jmidid) if you don't have that (i.e. Rosegarden outputs midi using ALSA and Pianoteq uses Jack Midi).
As another aside, if you are not running KXStudio, you might want to consider it as it is set up in a way that it overcomes a great many issues.
